Last updated: 2019-04-03

workflowr checks: (Click a bullet for more information)

• ✔ R Markdown file: up-to-date

  Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

• ✔ Repository version: 5870e6e

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

  
  Ignored files:
      Ignored:    .DS_Store
      Ignored:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    ._.DS_Store
      Ignored:    analysis/cache/
      Ignored:    build-logs/
      Ignored:    data/alevin/
      Ignored:    data/cellranger/
      Ignored:    data/processed/
      Ignored:    data/published/
      Ignored:    output/.DS_Store
      Ignored:    output/._.DS_Store
      Ignored:    output/03-clustering/selected_genes.csv.zip
      Ignored:    output/04-marker-genes/de_genes.csv.zip
      Ignored:    packrat/.DS_Store
      Ignored:    packrat/._.DS_Store
      Ignored:    packrat/lib-R/
      Ignored:    packrat/lib-ext/
      Ignored:    packrat/lib/
      Ignored:    packrat/src/
  
  Untracked files:
      Untracked:  DGEList.Rds
      Untracked:  output/90-methods/package-versions.json
      Untracked:  scripts/build.pbs
  
  Unstaged changes:
      Modified:   analysis/_site.yml
      Modified:   output/01-preprocessing/droplet-selection.pdf
      Modified:   output/01-preprocessing/parameters.json
      Modified:   output/01-preprocessing/selection-comparison.pdf
      Modified:   output/01B-alevin/alevin-comparison.pdf
      Modified:   output/01B-alevin/parameters.json
      Modified:   output/02-quality-control/qc-thresholds.pdf
      Modified:   output/02-quality-control/qc-validation.pdf
      Modified:   output/03-clustering/cluster-comparison.pdf
      Modified:   output/03-clustering/cluster-validation.pdf
      Modified:   output/04-marker-genes/de-results.pdf
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	33ac14f	Luke Zappia	2019-03-20	Tidy up website
html	33ac14f	Luke Zappia	2019-03-20	Tidy up website
html	fb2eb66	Luke Zappia	2019-01-10	Tidy workflowr and packrat setup
Rmd	8b1bef9	Luke Zappia	2019-01-10	Start workflowr project.

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The code in this analysis is covered by the GNU General Public License v3.0 and the written content on this website is covered by a Creative Commons CC-BY license.

The publications mentioned and datasets used are covered by their respective licenses and usage agreements. Please refer to those sources for details.

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This reproducible R Markdown analysis was created with workflowr 1.1.1

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